The agency says the J.C. Wilt Infectious Diseases Research Centre will complement the agency's existing National Microbiology Laboratory in the city by providing extra capacity for diagnostic testing during emergencies.
It will also carry out early vaccine development research, and act as a hub for HIV and AIDS research.
The centre was named in honour of Dr. John Charles Wilt, who was a pioneer of infectious disease research in Winnipeg.
The agency says the centre features some of the most advanced laboratory training facilities in the world and will accommodate up to 200 highly skilled employees.
It includes a training area dedicated to high-containment, or Level 4, laboratory environments.
"This new state-of-the-art research centre reaffirms and strengthens Canada's position as a leader in science and research at home and around the world," Health Minister Rona Ambrose said Friday in a news release.
The building where the research centre is located was previously a provincially-owned laboratory. The retrofit design started in 2008 and construction began in March 2011.
Dr. Greg Taylor, Canada's deputy chief public heath officer, said the facility will attract leading infectious disease scientists to the city.
"Winnipeg has become a global force in infectious disease research and this new facility adds to that reputation," he said.